Abstract
The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during evolution. Here, genome-wide gene order information was compiled for 64 species, representing a wide variety of eukaryotic phyla. This information is presented in a browser where gene order may be displayed and compared between species. Factors related to non-random gene order in eukaryotes were examined by considering pairs of neighboring genes. The evolutionary conservation of gene pairs was studied with respect to relative transcriptional direction, intergenic distance and functional relationship as inferred by gene ontology. The results show that among gene pairs that are conserved the divergently and co-directionally transcribed genes are much more common than those that are convergently transcribed. Furthermore, highly conserved pairs, in particular those of fungi, are characterized by a short intergenic distance. Finally, gene pairs of metazoa and fungi that are evolutionary conserved and that are divergently transcribed are much more likely to be related by function as compared to poorly conserved gene pairs. One example is the ribosomal protein gene pair L13/S16, which is unusual as it occurs both in fungi and alveolates. A specific functional relationship between these two proteins is also suggested by the fact that they are part of the same operon in both eubacteria and archaea. In conclusion, factors associated with non-random gene order in eukaryotes include relative gene orientation, intergenic distance and functional relationships. It seems likely that certain pairs of genes are conserved because the genes involved have a transcriptional and/or functional relationship. The results also indicate that studies of gene order conservation aid in identifying genes that are related in terms of transcriptional control.
Highlights
Recombination events result in shuffling of genes in genomes during evolution
We focused on a set of parameters of interest to gene order; relative transcription direction, intergenic distance, and functional relationships as inferred from gene ontology and we examined the relationship of these three parameters to evolutionary conservation
The OrthoMCL clustering generated a total of 71,219 clusters, involving 652,857 proteins
Summary
Recombination events result in shuffling of genes in genomes during evolution. Eukaryotes, are not subject to this restriction and gene order is to a large extent random. If we compare two eukaryotic genomes that are only distantly related, it is very unlikely that two genes are in the same order in the two species. Gene order is not completely random in eukaryotes. An intriguing case is a gene cluster in Saccharomyces cerevisiae that enables the use of allantoin as nitrogen source. In this case an evolution is observed where genes that were previously scattered around the genome became relocated to a single site in an ancestor of S
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
